AMP ISV in Somatic Conditions - Reporting

Reporting Survey

Question Title

* 1. What is your occupation/role?

Pathologist

Physician

Oncologist

Researcher

Bioinformatician

Laboratory Medical Director

Laboratory Supervisor

Pathologist Assistant

Clinical Laboratory Technologist / Technician

Other (please specify)

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* 2. What types of information do you include in your literature search (choose all that apply)?

Frequency in cancer - general

Frequency in cancer - specific tumor subtypes

Functional studies - activating

Functional studies - loss of function

Cellular pathway information

Review of pre-clinical studies

Review of clinical trials/pharmacogenomics

Level of specificity (variant-tumor type, gene-tumor type, considerations for histologic variants, etc).

Other (please specify)

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* 3. How do you classify your variants:

Five category system: Pathogenic, Likely pathogenic, VUS, Likely benign, Benign

Three category system: Pathogenic, VUS, Benign

Other (please specify)

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* 4. What variants are included in final report (select all that apply)?

Pathogenic mutations/variants

Likely pathogenic mutations/variants

VUS

Likely benign

Benign

Other (please specify)

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* 5. How do you group mutations/variants in the report (select all that apply)?

Actionable mutations: therapeutic, predictive, diagnostic, prognostic

Potentially actionable mutations: mutations in genes involved in the tumor associated pathways; off-label use of FDA approved drugs

Mutations in other cancer genes

Mutations in non-cancer genes

Other (please specify)

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* 6. Do you use a commercially available template for your reports?

Yes

if yes, please list which vendor

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* 7. Do you report therapeutic implications linked to your findings?

Yes

sometimes

if sometimes, please list under what conditions this is done

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* 8. which databases do you use to report the therapeutic implications of the variants that are identified?(check all that apply)

mycancergenome

OMIM

Gene specific literature search

Clinical significance included in commercial reporting package

ClinicalTrials.gov

Other (please specify)

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* 9. How do you report negative results in relevant cancer genes?

Tabular summary with gene symbol only

Tabular summary with gene symbol and/or hotspot information

Not included in report but linked to online resource/website

This information is not provided

Other (please specify)

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* 10. How are potential germline variants in known inherited cancer related genes reported in tumor sequencing tests?

Never reported

Never reported but an appropriate disclaimer is part of the report

Possibility suggested and/or genetic counseling is recommended in the report with an appropriate disclaimer

Information is reported with confirmation on normal tissue/blood sample

Information is discussed with clinical team in addition to inclusion in final report

Other (please specify)

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* 11. Is genomic coordinate included in clinical report for listing/summarizing variants?

Yes

Comment

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* 12. Is transcript accession version (e.g NM_004333.4 for BRAF gene) information included in the report when using HGVS nomenclature for reporting variants?

Yes

Comment

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* 13. Information on which of the following is included in the clinical report?

sequencing/library prep kits

analytic pipeline(s)

databases

informatics tools

Comment

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* 14. Do you report relative allele frequencies of the variants?

Yes

Comment

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* 15. Do you report genes/regions in which results did not meet your QC standards for a particular sample and for which a false negative variant result may be generated?

Yes, but only for actionable/targeted variant regions

Yes, for all possible regions

Comment

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* 16. Would you be willing to share your report format with this project?

Yes

Please provide contact information

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* 17. Do you perform and report RNA based NGS testing? If so, what bioinformatics pipeline is used for analyzing and reporting such data?

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* 18. How do you bill your NGS tests?

NGS codes

clinically actionable genes/variants only

balance billing

Other (please specify)

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* 19. Please add any information you feel would be beneficial to provide in this survey.

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* 20. (Optional) Please provide your name and email address to enable us to contact you in the future. The information will strictly be used only for the purpose of this survey.